FMO DATABASE

FMODB ID: 9GZM2

Calculation Name: 3F1I-H-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3F1I

Chain ID: H

ChEMBL ID:
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UniProt ID: O14964

Base Structure: X-ray

Registration Date: 2023-06-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	98
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-554481.13284
FMO2-HF: Nuclear repulsion	514540.616375
FMO2-HF: Total energy	-39940.516465
FMO2-MP2: Total energy	-40056.968237

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(H:404:SER)

Summations of interaction energy for fragment #1(H:404:SER)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-19.427	-14.931	6.228	-4.484	-6.241	0.029

Interaction energy analysis for fragmet #1(H:404:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.014

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	H	406	GLU	-1	-0.922	-0.959	2.528	-1.001	1.746	1.151	-1.449	-2.449	0.008
4	H	407	GLN	0	-0.069	-0.026	2.222	-9.774	-9.052	5.058	-2.487	-3.294	0.018
5	H	408	PHE	0	0.030	-0.003	3.453	-2.885	-1.858	0.019	-0.548	-0.498	0.003
6	H	409	LEU	0	0.040	0.015	5.459	-0.677	-0.677	0.000	0.000	0.000	0.000
7	H	410	LYS	1	0.965	0.983	5.919	-3.262	-3.262	0.000	0.000	0.000	0.000
8	H	411	ALA	0	-0.015	0.010	7.863	-0.446	-0.446	0.000	0.000	0.000	0.000
9	H	412	LEU	0	0.057	0.022	9.456	-0.312	-0.312	0.000	0.000	0.000	0.000
10	H	413	GLN	0	0.013	-0.001	11.445	-0.144	-0.144	0.000	0.000	0.000	0.000
11	H	414	ASN	0	0.016	0.005	12.038	-0.209	-0.209	0.000	0.000	0.000	0.000
12	H	415	ALA	0	0.012	0.022	13.584	-0.139	-0.139	0.000	0.000	0.000	0.000
13	H	416	VAL	0	0.045	0.018	15.444	-0.109	-0.109	0.000	0.000	0.000	0.000
14	H	417	THR	0	-0.024	-0.019	16.998	-0.093	-0.093	0.000	0.000	0.000	0.000
15	H	418	THR	0	-0.043	-0.038	17.477	-0.075	-0.075	0.000	0.000	0.000	0.000
16	H	419	PHE	0	-0.013	-0.002	19.422	-0.055	-0.055	0.000	0.000	0.000	0.000
17	H	420	VAL	0	0.042	0.015	21.238	-0.047	-0.047	0.000	0.000	0.000	0.000
18	H	421	ASN	0	-0.010	-0.015	22.790	-0.051	-0.051	0.000	0.000	0.000	0.000
19	H	422	ARG	1	0.893	0.939	23.802	-0.315	-0.315	0.000	0.000	0.000	0.000
20	H	423	MET	0	-0.020	-0.006	24.135	-0.033	-0.033	0.000	0.000	0.000	0.000
21	H	424	LYS	1	0.957	0.987	26.273	-0.292	-0.292	0.000	0.000	0.000	0.000
22	H	425	SER	0	0.034	0.015	28.203	-0.019	-0.019	0.000	0.000	0.000	0.000
23	H	426	ASN	0	-0.075	-0.052	28.493	-0.029	-0.029	0.000	0.000	0.000	0.000
24	H	427	HIS	0	0.083	0.051	31.552	-0.008	-0.008	0.000	0.000	0.000	0.000
25	H	428	MET	0	-0.034	-0.026	32.854	-0.006	-0.006	0.000	0.000	0.000	0.000
26	H	429	ARG	1	0.885	0.962	29.960	-0.199	-0.199	0.000	0.000	0.000	0.000
27	H	430	GLY	0	0.003	0.017	36.045	-0.008	-0.008	0.000	0.000	0.000	0.000
28	H	431	ARG	1	0.840	0.913	31.433	-0.178	-0.178	0.000	0.000	0.000	0.000
29	H	432	SER	0	0.047	0.022	34.446	0.009	0.009	0.000	0.000	0.000	0.000
30	H	433	ILE	0	0.050	-0.004	28.453	0.003	0.003	0.000	0.000	0.000	0.000
31	H	434	THR	0	0.010	0.013	29.739	0.010	0.010	0.000	0.000	0.000	0.000
32	H	435	ASN	0	-0.023	-0.008	31.752	-0.005	-0.005	0.000	0.000	0.000	0.000
33	H	436	ASP	-1	-0.858	-0.909	27.080	0.249	0.249	0.000	0.000	0.000	0.000
34	H	437	SER	0	0.041	0.021	27.011	0.016	0.016	0.000	0.000	0.000	0.000
35	H	438	ALA	0	0.039	0.009	22.926	0.014	0.014	0.000	0.000	0.000	0.000
36	H	439	VAL	0	-0.021	-0.008	22.376	0.033	0.033	0.000	0.000	0.000	0.000
37	H	440	LEU	0	0.033	0.025	23.180	0.021	0.021	0.000	0.000	0.000	0.000
38	H	441	SER	0	0.015	0.013	20.340	0.024	0.024	0.000	0.000	0.000	0.000
39	H	442	LEU	0	0.011	-0.002	17.440	0.033	0.033	0.000	0.000	0.000	0.000
40	H	443	PHE	0	0.001	-0.002	18.709	0.038	0.038	0.000	0.000	0.000	0.000
41	H	444	GLN	0	-0.007	-0.004	19.890	0.001	0.001	0.000	0.000	0.000	0.000
42	H	445	SER	0	-0.003	-0.009	14.935	0.031	0.031	0.000	0.000	0.000	0.000
43	H	446	ILE	0	-0.031	-0.011	14.981	0.071	0.071	0.000	0.000	0.000	0.000
44	H	447	ASN	0	-0.014	-0.009	16.096	0.024	0.024	0.000	0.000	0.000	0.000
45	H	448	GLY	0	-0.021	0.002	15.824	-0.024	-0.024	0.000	0.000	0.000	0.000
46	H	449	MET	0	-0.020	-0.021	11.001	0.090	0.090	0.000	0.000	0.000	0.000
47	H	450	HIS	0	-0.003	0.007	12.693	0.076	0.076	0.000	0.000	0.000	0.000
48	H	451	PRO	0	0.053	0.020	14.450	-0.005	-0.005	0.000	0.000	0.000	0.000
49	H	452	GLN	0	0.060	0.047	5.761	0.000	0.000	0.000	0.000	0.000	0.000
50	H	453	LEU	0	-0.048	-0.036	11.064	0.011	0.011	0.000	0.000	0.000	0.000
51	H	454	LEU	0	-0.020	-0.010	12.477	-0.061	-0.061	0.000	0.000	0.000	0.000
52	H	455	GLU	-1	-0.893	-0.942	11.924	0.204	0.204	0.000	0.000	0.000	0.000
53	H	456	LEU	0	-0.058	-0.034	7.406	-0.088	-0.088	0.000	0.000	0.000	0.000
54	H	457	LEU	0	-0.035	-0.020	11.440	-0.060	-0.060	0.000	0.000	0.000	0.000
55	H	458	ASN	0	0.064	0.044	14.736	-0.032	-0.032	0.000	0.000	0.000	0.000
56	H	459	GLN	0	-0.003	-0.008	11.419	-0.107	-0.107	0.000	0.000	0.000	0.000
57	H	460	LEU	0	-0.038	-0.019	12.081	-0.057	-0.057	0.000	0.000	0.000	0.000
58	H	461	ASP	-1	-0.864	-0.928	14.806	0.072	0.072	0.000	0.000	0.000	0.000
59	H	462	GLU	-1	-0.941	-0.975	16.563	-0.156	-0.156	0.000	0.000	0.000	0.000
60	H	463	ARG	1	0.865	0.933	11.890	0.370	0.370	0.000	0.000	0.000	0.000
61	H	464	ARG	1	0.847	0.930	17.253	-0.032	-0.032	0.000	0.000	0.000	0.000
62	H	465	LEU	0	0.034	0.014	19.841	-0.002	-0.002	0.000	0.000	0.000	0.000
63	H	466	TYR	0	-0.051	-0.017	19.903	-0.004	-0.004	0.000	0.000	0.000	0.000
64	H	467	TYR	0	-0.005	-0.023	17.464	-0.003	-0.003	0.000	0.000	0.000	0.000
65	H	468	GLU	-1	-0.872	-0.928	22.702	0.000	0.000	0.000	0.000	0.000	0.000
66	H	469	GLY	0	0.076	0.056	25.221	0.003	0.003	0.000	0.000	0.000	0.000
67	H	470	LEU	0	-0.076	-0.043	23.769	0.001	0.001	0.000	0.000	0.000	0.000
68	H	471	GLN	0	-0.008	-0.022	26.849	0.003	0.003	0.000	0.000	0.000	0.000
69	H	472	ASP	-1	-0.865	-0.927	28.658	-0.031	-0.031	0.000	0.000	0.000	0.000
70	H	473	LYS	1	0.928	0.963	29.837	0.098	0.098	0.000	0.000	0.000	0.000
71	H	474	LEU	0	-0.017	-0.016	29.303	0.002	0.002	0.000	0.000	0.000	0.000
72	H	475	ALA	0	-0.019	0.009	32.778	0.004	0.004	0.000	0.000	0.000	0.000
73	H	476	GLN	0	0.041	0.012	34.902	-0.002	-0.002	0.000	0.000	0.000	0.000
74	H	477	ILE	0	-0.016	-0.001	33.773	0.001	0.001	0.000	0.000	0.000	0.000
75	H	478	ARG	1	0.922	0.966	35.859	0.027	0.027	0.000	0.000	0.000	0.000
76	H	479	ASP	-1	-0.880	-0.946	38.707	-0.026	-0.026	0.000	0.000	0.000	0.000
77	H	480	ALA	0	-0.008	0.008	40.550	0.002	0.002	0.000	0.000	0.000	0.000
78	H	481	ARG	1	0.913	0.951	41.351	0.047	0.047	0.000	0.000	0.000	0.000
79	H	482	GLY	0	0.024	0.002	42.859	0.002	0.002	0.000	0.000	0.000	0.000
80	H	483	ALA	0	0.026	0.016	44.743	0.002	0.002	0.000	0.000	0.000	0.000
81	H	484	LEU	0	0.005	0.000	45.837	0.001	0.001	0.000	0.000	0.000	0.000
82	H	485	SER	0	-0.071	-0.047	46.495	0.000	0.000	0.000	0.000	0.000	0.000
83	H	486	ALA	0	0.004	0.009	48.937	0.001	0.001	0.000	0.000	0.000	0.000
84	H	487	LEU	0	0.056	0.034	49.798	0.001	0.001	0.000	0.000	0.000	0.000
85	H	488	ARG	1	0.884	0.941	48.179	0.038	0.038	0.000	0.000	0.000	0.000
86	H	489	GLU	-1	-0.873	-0.936	53.199	-0.020	-0.020	0.000	0.000	0.000	0.000
87	H	490	GLU	-1	-0.804	-0.877	54.967	-0.018	-0.018	0.000	0.000	0.000	0.000
88	H	491	HIS	0	-0.036	-0.027	56.420	0.001	0.001	0.000	0.000	0.000	0.000
89	H	492	ARG	1	0.906	0.939	53.232	0.026	0.026	0.000	0.000	0.000	0.000
90	H	493	GLU	-1	-0.936	-0.966	57.930	-0.015	-0.015	0.000	0.000	0.000	0.000
91	H	494	LYS	1	0.835	0.892	59.412	0.019	0.019	0.000	0.000	0.000	0.000
92	H	495	LEU	0	-0.031	-0.013	61.195	0.000	0.000	0.000	0.000	0.000	0.000
93	H	496	ARG	1	0.894	0.960	59.400	0.017	0.017	0.000	0.000	0.000	0.000
94	H	497	ARG	1	1.016	1.010	63.903	0.014	0.014	0.000	0.000	0.000	0.000
95	H	498	ALA	0	-0.037	-0.020	67.049	0.001	0.001	0.000	0.000	0.000	0.000
96	H	499	ALA	0	-0.034	-0.011	68.443	0.000	0.000	0.000	0.000	0.000	0.000
97	H	500	GLU	-1	-0.996	-1.001	67.971	-0.013	-0.013	0.000	0.000	0.000	0.000
98	H	501	GLU	-1	-1.025	-0.988	71.793	-0.011	-0.011	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(H:404:SER)